Variant report

Variant	rs10758787
Chromosome Location	chr9:6418829-6418830
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:6418658-6419098	GM12878	blood:	n/a	n/a
2	POLR2A	chr9:6418751-6419110	GM12892	blood:	n/a	n/a
3	POLR2A	chr9:6418697-6419120	GM12892	blood:	n/a	n/a
4	PML	chr9:6418424-6419136	GM12878	blood:	n/a	n/a
5	MYC	chr9:6418783-6418959	MCF10A-Er-Src	breast:	n/a	n/a
6	BCLAF1	chr9:6418482-6419128	GM12878	blood:	n/a	n/a
7	YY1	chr9:6418781-6419129	GM12892	blood:	n/a	n/a
8	TBL1XR1	chr9:6418787-6419138	GM12878	blood:	n/a	n/a
9	POLR2A	chr9:6418797-6418918	GM12878	blood:	n/a	n/a
10	YY1	chr9:6418654-6419151	GM12878	blood:	n/a	chr9:6418766-6418776
11	TBP	chr9:6418719-6419358	GM12878	blood:	n/a	n/a
12	YY1	chr9:6418811-6419203	GM12892	blood:	n/a	n/a
13	POLR2A	chr9:6418730-6419069	GM12892	blood:	n/a	n/a
14	USF2	chr9:6418809-6419116	GM12878	blood:	n/a	n/a
15	USF1	chr9:6418828-6419089	H1-hESC	embryonic stem cell:	n/a	n/a
16	YY1	chr9:6418775-6419163	GM12878	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:6412168..6415418-chr9:6418500..6425043,7	MCF-7	breast:
2	chr9:6412902..6414944-chr9:6415944..6418989,4	MCF-7	breast:
3	chr9:6417024..6418829-chr9:6426585..6429333,3	K562	blood:
4	chr9:6417292..6420636-chr9:6422611..6425827,4	K562	blood:
5	chr9:6417367..6418926-chr9:6465280..6467264,2	MCF-7	breast:
6	chr9:6417900..6420636-chr9:6424327..6426106,2	K562	blood:
7	chr9:6412634..6415362-chr9:6415861..6419998,11	K562	blood:

No data

Variant related genes	Relation type
UHRF2	TF binding region
ENSG00000147854	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10115362	0.87[ASN][1000 genomes]
rs10124572	0.86[ASN][1000 genomes]
rs10733529	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10739098	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10739099	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10739100	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10739102	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10758783	0.85[ASN][1000 genomes]
rs10758784	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10758785	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10758786	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10758788	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10758789	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10758790	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10758791	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10758792	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10815428	0.86[ASN][1000 genomes]
rs10815435	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10975579	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10975582	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10975583	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10975585	0.94[ASN][1000 genomes]
rs10975595	0.86[ASN][1000 genomes]
rs1156747	0.93[ASN][1000 genomes]
rs11790625	0.88[ASN][1000 genomes]
rs11791651	0.83[ASN][1000 genomes]
rs12346455	0.84[ASN][1000 genomes]
rs12351293	0.86[ASN][1000 genomes]
rs12376117	0.85[ASN][1000 genomes]
rs13292799	0.89[ASN][1000 genomes]
rs13440427	0.82[ASN][1000 genomes]
rs1381035	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1381036	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1381037	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16924562	0.85[ASN][1000 genomes]
rs16924591	0.85[ASN][1000 genomes]
rs1824537	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1870696	0.84[ASN][1000 genomes]
rs1903419	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2065074	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2065075	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2169283	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2169286	0.94[ASN][1000 genomes]
rs2381444	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3739654	0.83[ASN][1000 genomes]
rs380674	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs394137	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs414107	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4380997	0.81[ASN][1000 genomes]
rs4384035	0.87[ASN][1000 genomes]
rs452135	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4556138	0.82[ASN][1000 genomes]
rs4740844	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4740845	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4742199	0.98[ASN][1000 genomes]
rs4742201	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4742202	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4742204	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs504698	0.85[ASN][1000 genomes]
rs530722	0.83[ASN][1000 genomes]
rs55960819	0.86[ASN][1000 genomes]
rs56218473	0.91[ASN][1000 genomes]
rs56396114	0.86[ASN][1000 genomes]
rs56939673	0.90[ASN][1000 genomes]
rs569866	0.85[ASN][1000 genomes]
rs6477086	0.81[ASN][1000 genomes]
rs67852216	0.87[ASN][1000 genomes]
rs7027302	0.86[ASN][1000 genomes]
rs7033940	0.85[ASN][1000 genomes]
rs73401679	0.85[ASN][1000 genomes]
rs7853059	0.85[ASN][1000 genomes]
rs7853834	0.85[ASN][1000 genomes]
rs7857628	0.84[ASN][1000 genomes]
rs7860427	0.87[ASN][1000 genomes]
rs7860966	0.90[ASN][1000 genomes]
rs7861073	0.90[ASN][1000 genomes]
rs7861559	0.90[ASN][1000 genomes]
rs7865955	0.85[ASN][1000 genomes]
rs7871134	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031086	chr9:5806949-6630686	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv539967	chr9:5806949-6630686	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv933124	chr9:6099101-6644738	Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv1029000	chr9:6188652-6687205	Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
5	nsv1031459	chr9:6216913-6657192	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv948562	chr9:6222553-6684955	Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
7	nsv1032350	chr9:6328167-6630686	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv892160	chr9:6364449-6506038	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv892161	chr9:6364449-6523056	Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
10	nsv831497	chr9:6377501-6612402	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10758787	C9orf38	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6414400-6427400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:6414600-6439400	Weak transcription	Colonic Mucosa	Colon
3	chr9:6414600-6449000	Weak transcription	Gastric	stomach
4	chr9:6414600-6449200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr9:6414600-6451800	Weak transcription	Esophagus	oesophagus
6	chr9:6414600-6477800	Weak transcription	Placenta	Placenta
7	chr9:6414800-6422000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr9:6415400-6419400	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr9:6415400-6419600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr9:6415400-6419600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr9:6415400-6425400	Weak transcription	Psoas Muscle	Psoas
12	chr9:6415400-6434000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr9:6415600-6419200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr9:6415600-6419400	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr9:6415600-6419400	Enhancers	Primary B cells from cord blood	blood
16	chr9:6415600-6420800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr9:6415600-6421000	Weak transcription	Fetal Intestine Large	intestine
18	chr9:6415600-6422000	Weak transcription	Fetal Kidney	kidney
19	chr9:6415600-6422200	Weak transcription	Lung	lung
20	chr9:6415600-6423200	Weak transcription	Stomach Mucosa	stomach
21	chr9:6415600-6430000	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr9:6415600-6431000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr9:6415600-6441200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr9:6415600-6471400	Weak transcription	Aorta	Aorta
25	chr9:6415800-6419400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr9:6415800-6442800	Weak transcription	Stomach Smooth Muscle	stomach
27	chr9:6416000-6420000	Weak transcription	Fetal Intestine Small	intestine
28	chr9:6416000-6438400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr9:6416200-6419200	Enhancers	Brain Cingulate Gyrus	brain
30	chr9:6416200-6419800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr9:6416400-6419000	Enhancers	Fetal Brain Male	brain
32	chr9:6416400-6420600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr9:6416400-6421400	Weak transcription	Left Ventricle	heart
34	chr9:6416400-6421400	Weak transcription	Pancreas	Pancrea
35	chr9:6416400-6429800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr9:6416400-6430000	Weak transcription	Spleen	Spleen
37	chr9:6416400-6430600	Weak transcription	Right Ventricle	heart
38	chr9:6416400-6449200	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr9:6416600-6419000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr9:6416600-6419400	Enhancers	Primary B cells from peripheral blood	blood
41	chr9:6416600-6420000	Weak transcription	Fetal Thymus	thymus
42	chr9:6416600-6421400	Weak transcription	Fetal Muscle Leg	muscle
43	chr9:6416800-6419400	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr9:6417000-6419000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr9:6417000-6419000	Enhancers	Primary T cells from cord blood	blood
46	chr9:6417000-6419000	Enhancers	Duodenum Mucosa	Duodenum
47	chr9:6417000-6422200	Weak transcription	Fetal Stomach	stomach
48	chr9:6417200-6419200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr9:6417200-6419400	Enhancers	Primary T helper naive cells from peripheral blood	blood
50	chr9:6417200-6419400	Enhancers	Brain Anterior Caudate	brain

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